Energetics of the lattice: Packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules

Berger, Imre; Cai, Li; Chen, Liqing; Rich, Alexander

doi:10.1002/(sici)1097-0282(1997)44:3<257::aid-bip5>3.0.co;2-u

Cited by 11 publications

(11 citation statements)

References 31 publications

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“…The result of this association is a regularly shaped tetraplex, which has one additional base stacking interaction relative to the two isolated helices. Subsequent to NMR studies, this unusual DNA structure was confirmed and further characterized by X‐ray crystallography 34…”

Section: Introductionmentioning

confidence: 90%

Are structural biases at protein termini a signature of vectorial folding?

Laio

Micheletti

2005

Proteins

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Experimental investigations of the biosynthesis of a number of proteins have pointed out that part of the native structure may be acquired already during translation. We carried out a comprehensive statistical analysis of some average structural properties of proteins that have been put forward as possible signatures of this progressive buildup process. Contrary to a widespread belief, we found that there is no major propensity of the amino acids to form contacts with residues that are closer to the N-terminus. Moreover, we found that the C-terminus is significantly more compact and locally organized than the N-terminus. This bias, though, is unlikely to be related to vectorial effects, since it correlates with subtle differences in the primary sequence. These findings indicate that even if proteins acquire their structure vectorially, no signature of this seems to be detectable in their average structural properties.

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Section: Introductionmentioning

confidence: 90%

Are structural biases at protein termini a signature of vectorial folding?

Laio

Micheletti

2005

Proteins

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“…In the crystalline state, however, a set of additional interactions are formed between molecules in close contact in the lattice, the packing interactions. This fact was shown by Berger and col. in the study of the crystal structures of C3T, TA2C3, C3A2T, and A2C4 33 . These molecules showed intercalated C segments that were similar in their geometry, even though the sequences crystallized in different space groups.…”

Section: Instrumental Approaches To Study the I-motif Structuresmentioning

confidence: 99%

Fundamental aspects of the nucleic acid i-motif structures

et al. 2014

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“…Non-cytosine nucleotides present in C-rich sequences can also affect the formation and stability of the i-motif structure through base interaction or stacking. For example, thymines in the sequences d(CCCT) [22], d(5mCCTCTCTCC) [23], d(5mCCTC n TCC) (n=1, 2, 3) [24] and d(5mCCTCC) [25] [26,27]. All of these non-C•C + base pairs add to the stability of structures.…”

Section: Introductionmentioning

confidence: 99%

Formation and Dissociation of the Interstrand i-Motif by the Sequences d(X_nC₄Y_m) Monitored with Electrospray Ionization Mass Spectrometry

Cao

Qin

Bruist

et al. 2015

J. Am. Soc. Mass Spectrom.

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Abstract. Formation and dissociation of the interstrand i-motifs by DNA with the sequence d(X n C 4 Y m ) (X and Y represent thymine, adenine, or guanine, and n, m range from 0 to 2) are studied with electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), and UV spectrophotometry. The ion complexes detected in the gas phase and the melting temperatures (T m ) obtained in solution show that a non-C base residue located at 5′ end favors formation of the four-stranded structures, with T > A > G for imparting stability. Comparatively, no rule is found when a non-C base is located at the 3′ end. Detection of penta-and hexa-stranded ions indicates the formation of i-motifs with more than four strands. In addition, the i-motifs seen in our mass spectra are accompanied by single-, double-, and triple-stranded ions, and the trimeric ions were always less abundant during annealing and heat-induced dissociation process of the DNA strands in solution (pH=4.5). This provides a direct evidence of a strand-by-strand formation and dissociation pathway of the interstrand i-motif and formation of the triple strands is the rate-limiting step. In contrast, the trimeric ions are abundant when the tetramolecular ions are subjected to collision-induced dissociation (CID) in the gas phase, suggesting different dissociation behaviors of the interstrand i-motif in the gas phase and in solution. Furthermore, hysteretic UV absorption melting and cooling curves reveal an irreversible dissociation and association kinetic process of the interstrand i-motif in solution.

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Energetics of the lattice: Packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules

Cited by 11 publications

References 31 publications

Are structural biases at protein termini a signature of vectorial folding?

Are structural biases at protein termini a signature of vectorial folding?

Fundamental aspects of the nucleic acid i-motif structures

Formation and Dissociation of the Interstrand i-Motif by the Sequences d(X_nC₄Y_m) Monitored with Electrospray Ionization Mass Spectrometry

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Energetics of the lattice: Packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules

Cited by 11 publications

References 31 publications

Are structural biases at protein termini a signature of vectorial folding?

Are structural biases at protein termini a signature of vectorial folding?

Fundamental aspects of the nucleic acid i-motif structures

Formation and Dissociation of the Interstrand i-Motif by the Sequences d(XnC4Ym) Monitored with Electrospray Ionization Mass Spectrometry

Contact Info

Product

Resources

About

Formation and Dissociation of the Interstrand i-Motif by the Sequences d(X_nC₄Y_m) Monitored with Electrospray Ionization Mass Spectrometry